grinch | global report investigating novel coronavirus haplotypes

New variant report 2020-12-31



Data source and processing

This report is recent as of 2020-12-31 14:02 GMT. All SARS-CoV-2 sequences were downloaded from GISAID and genomes were de-duplicated based on GISAID sequence name – note that the publically available metadata may not fully allow us to de-duplicate by patient. Full data processing pipeline found here.

The sequences were then assigned lineages with pangolin v2.1.4, pangoLEARN version 2020-12-17-2.

Pangolin assigns B.1.1.7 to sequences with more than 4 of the 17 defining B.1.1.7 SNPs – defined here – and B.1.351 to any sequences with more than 3 of the 5 defining B.1.351 SNPs.

Table 1 | Summary of data

Lineage Country count Country Sequence count Earliest sequence Travel history
B.1.351 4 South_Africa 322, Switzerland 2, Finland 1, UK 1 326 2020-10-08
B.1.1.7 21 UK 4518, Denmark 33, Portugal 20, Italy 17, Netherlands 8, Ireland 7, Australia 4, Israel 4, South_Korea 3, India 3, Finland 2, Norway 2, USA 2, Hong_Kong 2, Spain 1, Sweden 1, Canada 1, Switzerland 1, Germany 1, Singapore 1, France 1 4632 2020-09-20

Lineage B.1.351

Caveat: Most locations outside the original focus have not reported sustained transmission and many cases have known travel links to the focal location. Increasing numbers of international cases is currently likely due to increased surveillance and vigilance.

Table B.1.351 | Lineage B.1.351

Statistic Information
Count 326
Likely origin South Africa
SNPs aa:orf1ab:K1655N
aa:S:D215G
aa:S:E484K
aa:S:N501Y
snp:C23664T

Figure 1 | Cumulative sequence count over time B.1.351

2020-12-31T14:54:59.016195 image/svg+xml Matplotlib v3.3.3, https://matplotlib.org/

Figure 2 | Date of earliest B.1.351 detected

2020-12-31T14:54:58.481745 image/svg+xml Matplotlib v3.3.3, https://matplotlib.org/

Figure 3 | Map of B.1.351 sequence counts

2020-12-31T14:54:58.709506 image/svg+xml Matplotlib v3.3.3, https://matplotlib.org/

Figure 4 | Sequence count per country B.1.351

2020-12-31T14:54:58.858161 image/svg+xml Matplotlib v3.3.3, https://matplotlib.org/

Figure 5 | Frequency B.1.351 in sequences produced since first new variant reported per country

2020-12-31T14:54:59.134342 image/svg+xml Matplotlib v3.3.3, https://matplotlib.org/

Figure 6 | B.1.351 count per country

2020-12-31T14:54:59.456430 image/svg+xml Matplotlib v3.3.3, https://matplotlib.org/

Figure 7 | Rolling average B.1.351 frequency per country

2020-12-31T14:54:59.257077 image/svg+xml Matplotlib v3.3.3, https://matplotlib.org/

Lineage B.1.1.7

Caveat: Most locations outside the original focus have not reported sustained transmission and many cases have known travel links to the focal location. Increasing numbers of international cases is currently likely due to increased surveillance and vigilance.

Table B.1.1.7 | Lineage B.1.1.7

Statistic Information
Count 4632
Likely origin United Kingdom
SNPs aa:orf1ab:T1001I
aa:orf1ab:A1708D
aa:orf1ab:I2230T
del:11288:9
del:21765:6
del:21991:3
aa:S:N501Y
aa:S:A570D
aa:S:P681H
aa:S:T716I
aa:S:S982A
aa:S:D1118H
aa:Orf8:Q27*
aa:Orf8:R52I
aa:Orf8:Y73C
aa:N:D3L
aa:N:S235F

Figure 8 | Cumulative sequence count over time B.1.1.7

2020-12-31T14:54:54.417844 image/svg+xml Matplotlib v3.3.3, https://matplotlib.org/

Figure 9 | Date of earliest B.1.1.7 detected

2020-12-31T14:54:53.529609 image/svg+xml Matplotlib v3.3.3, https://matplotlib.org/

Figure 10 | Map of B.1.1.7 sequence counts

2020-12-31T14:54:53.837397 image/svg+xml Matplotlib v3.3.3, https://matplotlib.org/

Figure 11 | Sequence count per country B.1.1.7

2020-12-31T14:54:54.157499 image/svg+xml Matplotlib v3.3.3, https://matplotlib.org/

Figure 12 | Frequency B.1.1.7 in sequences produced since first new variant reported per country

2020-12-31T14:54:54.653213 image/svg+xml Matplotlib v3.3.3, https://matplotlib.org/

Figure 13 | B.1.1.7 count per country

2020-12-31T14:54:55.114374 image/svg+xml Matplotlib v3.3.3, https://matplotlib.org/

Figure 14 | Rolling average B.1.1.7 frequency per country

2020-12-31T14:54:54.905697 image/svg+xml Matplotlib v3.3.3, https://matplotlib.org/

Figure 11 | Air traffic from UK by destination

The number of ticketed origin-to-destination journeys from London airports to countries outside the United Kingdom during October 2020.

Colours indicate numbers of published genomes of B.1.1.7 deposited on GISAID. Grey bars indicate countries that have reported the presence of the variant but have not yet published B.1.1.7 sequences on GISAID. White bars indicate countries with no reports of B.1.1.7.

Flight data come from the International Air Transportation Association that capture anonymized, passenger-level flight itinerary data, comprising both commercial flights and scheduled charter flights. These data account for ~90% of global air travel volumes, with the remaining volumes modelled using market intelligence. We report data from destinations including >5,000 passengers.

Data from Kamran Khan, Isaac Bogoch, Alexander Watts, Oliver Pybus, Moritz Kraemer

2020-12-31T14:54:53.085658 image/svg+xml Matplotlib v3.3.3, https://matplotlib.org/